PC/Mac Seq Comps: Digest

Tom DeVrie tomdevrie at aol.com
Mon Jul 31 15:50:15 EST 1995


A brief digest follows of paraphrased responses to my request for PC/Mac
programs for comparing sequences and constructing phylogenetic trees. 
Thanks to those who kindly supplied this information.
__________
The most widely used sequence alignment program is CCLUSTAL. Runs on PCs.
A selfextractable file can be obtained by anonymous FTP from
ftp.ebi.ac.uk. 

unix      pub/software/unix/clustalw.tar.Z  (compressed tar archive)
vms       pub/software/vms/clustalw.uue     (uuencoded ZIP archive)
mac       pub/software/mac/clustalw.sea.hqx (self extracting 
archive/binhex)
PC        pub/software/dos/clustal$.exe     (self extracting ZIP archive)
__________
The FASTA package, in particular SSEARCH and ALIGN, will do alignments. 
Available for Unix, DOS, and Mac's from: ftp.virginia.edu in pub/fasta.
__________
Felsenstein's PHYLIP package is available for Mac.  Also one for
Swofford's PAUP.  Check a bionet ftp sites. [n.b.:  Felsenstein has WWW
page: do net search on "Phylip."  Includes info on other phylogenetic
programs.]
__________
VOSTORG package at anonymous FTP at
gsbs18.gs.uth.tmc.edu/pub/zharkikh/vostorg

For IBM; has simple level of phylogenetic analysis. Includes sequence dot
matrix
comparison. alignment, distance matrix calculation and tree
reconstruction/ visualisation. It was used at our graduate courses and in
routine practice.
__________
DAPSA.  Contact HARLEY at chempath.uct.ac.za for more info.
__________
SeqPup, which when combined with ClustalW for
automatic alignment, is a free tool for biosequence analyses.
Fetch it at 
   <ftp://iubio.bio.indiana.edu/molbio/seqpup/>
   <gopher://iubio.bio.indiana.edu/11/IUBio-Software+Data/molbio/seqpup/>
   <http://iubio.bio.indiana.edu/1/IUBio-Software%2bData/molbio/seqpup/>

Caveat: it is still undergoing development, and its incomplete
state may make it unsuited for your need just now.  It will be
better off in a few months.
__________
There is DCSE (Dedicated Comparative Sequence Editor) for DOS. It does
what 
you want, though the Unix versions are a lot nicer. You might consider 
using Linux to run Unix programs on your PC. You can find more info on and
the distributions of DCSE on URL:
http://www-rrna.uia.ac.be/~peter/dcse
or use anonymous ftp to host indigo2.uia.ac.be



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